The Radioshack Leopard Trek rider was seven seconds behind after the first split but ended up romping to victory 59 seconds ahead of IAM Cycling's Martin Elmiger,with Reto Hollenstein (also IAN) third, 1:57 back, in hot conditions.
Cancellera has often been seen in time trials wearing the red with white cross colours of the Swiss flag after having also won this race in 2002, 2004-2008 and 2012.
"It was really, really hard. The course was up and down the whole time and with these temperatures, it made for a tough ride," said Cancellara.
"I still felt the Tour de Suisse in my legs, despite the good feelings on the bike yesterday. For me it was also a test to see where my shape is at. I'm certainly satisfied."
"It never gets boring to win your National Championships. For me it's an honour to wear the jersey, so I really went for it!"